I'm more interested about the fact that Canon has always had cross type AF pts outside of middle section.

They haven't always had it. It's a very recent addition for Canon.

Has the Nikon's decades old flange/mount design caused that??

No, what caused it is Nikon basically copying AF layout from older Canons (like 1Ds Mark II), which were 45 AF points, 9 cross right smack in the middle. Nikon did D3, with 51 AF points, and 15 cross right smack in the middle.

Since those days, Nikon has tweaked and improved it's AF. Canon has tried more comprehensive changes to it's AF, which backfired spectacularly with the 1D Mark III, which managed (along with Nikon coming out with D3) to wipe out Canon's domination in the pro sports market. They seem to have gotten it right with 5D Mark III (and, therefore, 1D X too?). I wouldn't be surprised if we see a completely new AF from Nikon in the next generation cameras.